Meryl

This is 'meryl', a near total rewrite of 'meryl' that appeared in both project kmer and Celera Assembler.

IMPORTANT: Get the latest meryl code from this repo. This is not compatible with old meryl dbs built from canu 1.8 or earlier. The new meryl is significantly faster than the previous version.

Change log (each with lots of bug fixes)

• v1.4.2: Direct kmer counting from bam / cram

• v1.4.1: One critical bug fix (bitArray) found right after v1.4 release

• v1.4: meryl compress kmers, experimental meryl2

• v1.3: meryl-lookup to lookup kmers

• v1.2: meryl-analyze to analyze kmers, meryl-simple for simpler kmer counts

• v1.1: Brand-new meryl! .mcdat and .mcidx file formats are no longer used. Meryl db is designed as a DIRECTORY, containing 64 binaries + 64 indexes (128 files)

Dependency

• gcc 10.2+ or clang 12+

Installation

• Release version: download a stable release version

  Platform	Filename
  Linux x86_64	meryl-1.4.2.Linux-amd64.tar.xz
  Linux arm64	meryl-1.4.2.Linux-arm64.tar.xz
  macOS Apple Silicon	meryl-1.4.2.Darwin-arm64.tar.xz
  macOS Intel	meryl-1.4.2.Darwin-amd64.tar.xz

  # Example for Linux-amd64
  wget https://github.com/marbl/meryl/releases/download/v1.4.2/meryl-1.4.2.Linux-amd64.tar.xz
  tar -xJf meryl-1.4.2.Linux-amd64.tar.xz
  export PATH=/path/to/meryl-1.4.2/bin:$PATH

• MacOS: after unpacking, run xattr -dr com.apple.quarantine meryl-1.4.2.Darwin-*/. On MDM-managed Macs, Gatekeeper might still block the binaries — build from source instead.

• Experimental tip (use git 2.25.1 or higher):

  git clone --recursive https://github.com/marbl/meryl.git
  
  # build
  cd meryl/src
  make -j 24
  export PATH=/path/to/meryl/build/bin:$PATH

Evaluate assemblies with k-mers and more

See Merqury.

Citing Meryl

We didn't want to suffer the world with yet another k-mer counting paper, so we stuffed meryl into the merqury methods:

Rhie, A., Walenz, B.P., Koren, S. et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21, 245 (2020). https://doi.org/10.1186/s13059-020-02134-9